Supplementary Table S1: Descriptive and diversity parameters of each simulated dataset. Page 2
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| Metasim 2 | |
| Solibacter usitatus Ellin6076 | 223 |
| Haliangium ochraceum DSM 14365 | 211 |
| Frankia sp. EAN1pec | 206 |
| Bradyrhizobium japonicum USDA 110 chromosome | 201 |
| Catenulispora acidiphila DSM 44928 | 201 |
| Bacillus licheniformis ATCC 14580 | 191 |
| Bradyrhizobium sp. BTAi1 | 186 |
| Chitinophaga pinensis DSM 2588 | 185 |
| Streptosporangium roseum DSM 43021 | 180 |
| Myxococcus xanthus DK 1622 chromosome | 180 |
| Trichodesmium erythraeum IMS101 | 179 |
| Actinosynnema mirum DSM 43827 | 179 |
| Gluconacetobacter diazotrophicus PAl 5 | 177 |
| Saccharopolyspora erythraea NRRL 2338 chromosome | 170 |
| Nostoc punctiforme PCC 73102 | 168 |
| Spirosoma linguale DSM 74 | 164 |
| Kribbella flavida DSM 17836 | 163 |
| Rhodococcus jostii RHA1 | 161 |
| Rhodopirellula baltica SH 1 chromosome | 159 |
| Frankia alni ACN14a | 157 |
| Clostridium beijerinckii NCIMB 8052 | 157 |
| Streptomyces griseus subsp. griseus NBRC 13350 | 157 |
| Bradyrhizobium sp. ORS278 | 156 |
| Methylobacterium nodulans ORS 2060 | 156 |
| Pseudomonas aeruginosa PAO1 chromosome | 151 |
| Mycobacterium marinum M | 149 |
| Mycobacterium smegmatis str. MC2 155 | 148 |
| Mycobacterium sp. JLS | 144 |
| Pseudomonas putida KT2440 chromosome | 143 |
| Acaryochloris marina MBIC11017 | 143 |
| Pseudomonas aeruginosa PA7 | 142 |
| Pseudomonas putida W619 | 142 |
| Rhodococcus erythropolis PR4 | 141 |
| Stackebrandtia nassauensis DSM 44728 chromosome | 138 |
| Mycobacterium sp. KMS | 138 |
| Cyanothece sp. PCC 7822 chromosome | 137 |
| Methylobacterium extorquens PA1 | 136 |
| Anabaena variabilis ATCC 29413 | 134 |
| Dyadobacter fermentans DSM 18053 | 134 |
| Mesorhizobium loti MAFF303099 chromosome | 134 |
| Pseudomonas syringae pv. syringae B728a | 134 |
| Hahella chejuensis KCTC 2396 chromosome | 134 |
| Pseudomonas fluorescens SBW25 chromosome | 132 |
| Nakamurella multipartita DSM 44233 | 132 |
| Alkaliphilus metalliredigens QYMF | 132 |
| Thermomonospora curvata DSM 43183 | 131 |
| Conexibacter woesei DSM 14684 | 131 |
| Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111 chromosome | 131 |
| Rhodopseudomonas palustris BisB18 | 130 |
| Flavobacterium johnsoniae UW101 | 129 |
| Corynebacterium glutamicum ATCC 13032 | 129 |
| Herpetosiphon aurantiacus ATCC 23779 chromosome | 129 |
| Nocardia farcinica IFM 10152 | 129 |
| Nostoc sp. PCC 7120 | 129 |
| Serratia proteamaculans 568 chromosome | 128 |
| Methylobacterium chloromethanicum CM4 | 128 |
| Xanthomonas oryzae pv. oryzae PXO99A | 128 |
| Burkholderia multivorans ATCC 17616 chromosome 2 | 126 |
| Sphingomonas wittichii RW1 | 126 |
| Photorhabdus luminescens subsp. laumondii TTO1 | 126 |
| Methylobacterium radiotolerans JCM 2831 | 125 |
| Shewanella piezotolerans WP3 chromosome | 124 |
| Shewanella baltica OS185 | 124 |
| Candidatus Koribacter versatilis Ellin345 | 124 |
| Bordetella petrii DSM 12804 | 123 |
| Mycobacterium ulcerans Agy99 | 122 |
| Klebsiella pneumoniae subsp. pneumoniae MGH 78578 | 121 |
| Methylobacterium populi BJ001 | 120 |
| Bordetella parapertussis 12822 | 120 |
| Bacillus cereus B4264 | 120 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 chromosome | 120 |
| Roseiflexus castenholzii DSM 13941 | 120 |
| Dickeya dadantii 3937 chromosome | 120 |
| Bacillus weihenstephanensis KBAB4 | 120 |
| Methylobacterium extorquens AM1 | 119 |
| Pseudomonas syringae pv. phaseolicola 1448A | 119 |
| Cyanothece sp. PCC 7424 | 119 |
| Pseudomonas entomophila L48 | 119 |
| Escherichia coli CFT073 | 118 |
| Anaeromyxobacter sp. K | 116 |
| Cytophaga hutchinsonii ATCC 33406 | 116 |
| Bacillus cereus AH187 | 116 |
| Photorhabdus asymbiotica chromosome | 115 |
| Bacillus anthracis str. Ames | 115 |
| Bacteroides vulgatus ATCC 8482 chromosome | 115 |
| Pseudomonas putida F1 | 115 |
| Azotobacter vinelandii DJ chromosome | 115 |
| Caulobacter segnis ATCC 21756 chromosome | 115 |
| Pedobacter heparinus DSM 2366 | 114 |
| Geobacter sp. M21 | 114 |
| Mycobacterium sp. MCS | 114 |
| Bacillus cereus ATCC 10987 | 114 |
| Desulfobacterium autotrophicum HRM2 | 114 |
| Rhodopseudomonas palustris HaA2 | 114 |
| Escherichia coli APEC O1 | 114 |
| Xanthomonas oryzae pv. oryzae MAFF 311018 | 114 |
| Pseudomonas syringae pv. tomato str. DC3000 chromosome | 113 |
| Gordonia bronchialis DSM 43247 | 113 |
| Escherichia coli UTI89 | 113 |
| Methanosarcina acetivorans C2A chromosome | 113 |
| Rhodopseudomonas palustris BisA53 | 113 |
| Bacillus cereus E33L | 113 |
| Colwellia psychrerythraea 34H | 112 |
| Polaromonas sp. JS666 | 112 |
| Planctomyces limnophilus DSM 3776 chromosome | 112 |
| Mycobacterium avium 104 | 112 |
| Frankia sp. CcI3 | 111 |
| Rhodoferax ferrireducens T118 | 111 |
| Shewanella woodyi ATCC 51908 | 111 |
| Rhodopseudomonas palustris CGA009 chromosome | 111 |
| Marinomonas sp. MWYL1 chromosome | 111 |
| Yersinia pestis biovar Microtus str. 91001 | 110 |
| Syntrophobacter fumaroxidans MPOB | 110 |
| Xanthomonas campestris pv. campestris str. 8004 chromosome | 110 |
| Thauera sp. MZ1T | 110 |
| Bacillus cereus AH820 | 110 |
| Salmonella enterica subsp. enterica serovar Typhi str. Ty2 chromosome | 110 |
| Escherichia coli E24377A | 109 |
| Shigella flexneri 2a str. 2457T | 109 |
| Rhizobium etli CIAT 652 | 109 |
| Chromobacterium violaceum ATCC 12472 | 109 |
| Yersinia pseudotuberculosis IP 32953 | 108 |
| Shewanella baltica OS195 | 108 |
| Xanthomonas axonopodis pv. citri str. 306 chromosome | 108 |
| Teredinibacter turnerae T7901 | 108 |
| Caulobacter crescentus CB15 | 108 |
| Bacteroides fragilis YCH46 chromosome | 108 |
| Escherichia coli str. K-12 substr. W3110 chromosome | 107 |
| Caulobacter sp. K31 chromosome | 107 |
| Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 chromosome | 107 |
| Bacillus thuringiensis str. Al Hakam | 107 |
| Paenibacillus polymyxa E681 chromosome | 106 |
| Pseudoalteromonas atlantica T6c |
